The genome sequence and effector complement of the flax rust pathogen Melampsora lini.
Identifieur interne : 000040 ( Main/Exploration ); précédent : 000039; suivant : 000041The genome sequence and effector complement of the flax rust pathogen Melampsora lini.
Auteurs : Adnane Nemri [Australie] ; Diane G O. Saunders [Royaume-Uni] ; Claire Anderson [Australie] ; Narayana M. Upadhyaya [Australie] ; Joe Win [Royaume-Uni] ; Gregory J. Lawrence [Australie] ; David A. Jones [Australie] ; Sophien Kamoun [Royaume-Uni] ; Jeffrey G. Ellis [Australie] ; Peter N. Dodds [Australie]Source :
- Frontiers in plant science [ 1664-462X ] ; 2014.
Abstract
Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.
DOI: 10.3389/fpls.2014.00098
PubMed: 24715894
PubMed Central: PMC3970004
Affiliations:
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Saunders</name><affiliation wicri:level="1"><nlm:affiliation>The Sainsbury Laboratory, Norwich Research Park Norwich, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sainsbury Laboratory, Norwich Research Park Norwich</wicri:regionArea><wicri:noRegion>Norwich Research Park Norwich</wicri:noRegion></affiliation></author><author><name sortKey="Anderson, Claire" sort="Anderson, Claire" uniqKey="Anderson C" first="Claire" last="Anderson">Claire Anderson</name><affiliation wicri:level="1"><nlm:affiliation>Research School of Biological Sciences, College of Medicine, Biology and Environment, Australian National University Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Research School of Biological Sciences, College of Medicine, Biology and Environment, Australian National University Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author><author><name sortKey="Upadhyaya, Narayana M" sort="Upadhyaya, Narayana M" uniqKey="Upadhyaya N" first="Narayana M" last="Upadhyaya">Narayana M. Upadhyaya</name><affiliation wicri:level="1"><nlm:affiliation>CSIRO Plant Industry Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Plant Industry Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author><author><name sortKey="Win, Joe" sort="Win, Joe" uniqKey="Win J" first="Joe" last="Win">Joe Win</name><affiliation wicri:level="1"><nlm:affiliation>The Sainsbury Laboratory, Norwich Research Park Norwich, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sainsbury Laboratory, Norwich Research Park Norwich</wicri:regionArea><wicri:noRegion>Norwich Research Park Norwich</wicri:noRegion></affiliation></author><author><name sortKey="Lawrence, Gregory J" sort="Lawrence, Gregory J" uniqKey="Lawrence G" first="Gregory J" last="Lawrence">Gregory J. Lawrence</name><affiliation wicri:level="1"><nlm:affiliation>CSIRO Plant Industry Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Plant Industry Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author><author><name sortKey="Jones, David A" sort="Jones, David A" uniqKey="Jones D" first="David A" last="Jones">David A. Jones</name><affiliation wicri:level="1"><nlm:affiliation>Research School of Biological Sciences, College of Medicine, Biology and Environment, Australian National University Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Research School of Biological Sciences, College of Medicine, Biology and Environment, Australian National University Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author><author><name sortKey="Kamoun, Sophien" sort="Kamoun, Sophien" uniqKey="Kamoun S" first="Sophien" last="Kamoun">Sophien Kamoun</name><affiliation wicri:level="1"><nlm:affiliation>The Sainsbury Laboratory, Norwich Research Park Norwich, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sainsbury Laboratory, Norwich Research Park Norwich</wicri:regionArea><wicri:noRegion>Norwich Research Park Norwich</wicri:noRegion></affiliation></author><author><name sortKey="Ellis, Jeffrey G" sort="Ellis, Jeffrey G" uniqKey="Ellis J" first="Jeffrey G" last="Ellis">Jeffrey G. Ellis</name><affiliation wicri:level="1"><nlm:affiliation>CSIRO Plant Industry Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Plant Industry Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author><author><name sortKey="Dodds, Peter N" sort="Dodds, Peter N" uniqKey="Dodds P" first="Peter N" last="Dodds">Peter N. Dodds</name><affiliation wicri:level="1"><nlm:affiliation>CSIRO Plant Industry Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Plant Industry Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">24715894</PMID><DateCompleted><Year>2014</Year><Month>04</Month><Day>09</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>The genome sequence and effector complement of the flax rust pathogen Melampsora lini.</ArticleTitle><Pagination><MedlinePgn>98</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2014.00098</ELocationID><Abstract><AbstractText>Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Nemri</LastName><ForeName>Adnane</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>CSIRO Plant Industry Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Saunders</LastName><ForeName>Diane G O</ForeName><Initials>DG</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, Norwich Research Park Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Anderson</LastName><ForeName>Claire</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Research School of Biological Sciences, College of Medicine, Biology and Environment, Australian National University Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Upadhyaya</LastName><ForeName>Narayana M</ForeName><Initials>NM</Initials><AffiliationInfo><Affiliation>CSIRO Plant Industry Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Win</LastName><ForeName>Joe</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, Norwich Research Park Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lawrence</LastName><ForeName>Gregory J</ForeName><Initials>GJ</Initials><AffiliationInfo><Affiliation>CSIRO Plant Industry Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jones</LastName><ForeName>David A</ForeName><Initials>DA</Initials><AffiliationInfo><Affiliation>Research School of Biological Sciences, College of Medicine, Biology and Environment, Australian National University Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kamoun</LastName><ForeName>Sophien</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, Norwich Research Park Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ellis</LastName><ForeName>Jeffrey G</ForeName><Initials>JG</Initials><AffiliationInfo><Affiliation>CSIRO Plant Industry Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dodds</LastName><ForeName>Peter N</ForeName><Initials>PN</Initials><AffiliationInfo><Affiliation>CSIRO Plant Industry Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>03</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Melampsora</Keyword><Keyword MajorTopicYN="N">avirulence</Keyword><Keyword MajorTopicYN="N">effector</Keyword><Keyword MajorTopicYN="N">flax</Keyword><Keyword MajorTopicYN="N">rust</Keyword><Keyword MajorTopicYN="N">virulence</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>01</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>02</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>4</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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name="Australie"><noRegion><name sortKey="Nemri, Adnane" sort="Nemri, Adnane" uniqKey="Nemri A" first="Adnane" last="Nemri">Adnane Nemri</name></noRegion><name sortKey="Anderson, Claire" sort="Anderson, Claire" uniqKey="Anderson C" first="Claire" last="Anderson">Claire Anderson</name><name sortKey="Dodds, Peter N" sort="Dodds, Peter N" uniqKey="Dodds P" first="Peter N" last="Dodds">Peter N. Dodds</name><name sortKey="Ellis, Jeffrey G" sort="Ellis, Jeffrey G" uniqKey="Ellis J" first="Jeffrey G" last="Ellis">Jeffrey G. Ellis</name><name sortKey="Jones, David A" sort="Jones, David A" uniqKey="Jones D" first="David A" last="Jones">David A. Jones</name><name sortKey="Lawrence, Gregory J" sort="Lawrence, Gregory J" uniqKey="Lawrence G" first="Gregory J" last="Lawrence">Gregory J. Lawrence</name><name sortKey="Upadhyaya, Narayana M" sort="Upadhyaya, Narayana M" uniqKey="Upadhyaya N" first="Narayana M" last="Upadhyaya">Narayana M. Upadhyaya</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Saunders, Diane G O" sort="Saunders, Diane G O" uniqKey="Saunders D" first="Diane G O" last="Saunders">Diane G O. Saunders</name></noRegion><name sortKey="Kamoun, Sophien" sort="Kamoun, Sophien" uniqKey="Kamoun S" first="Sophien" last="Kamoun">Sophien Kamoun</name><name sortKey="Win, Joe" sort="Win, Joe" uniqKey="Win J" first="Joe" last="Win">Joe Win</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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